A new BODIPY system displaying an intramolecular π-π-interaction was synthesized and studied. When the selenium center was oxidized, the substituted phenyl group undergoes π-π stacking with one side of the BODIPY core. The oxidized form showed, not only a down-field shift in the NMR peak, but also splitting due to geometrical changes that arise when going from Cs to C1. The compound was characterized by X-ray diffraction; DFT methods helped elucidate the influence of the unexpected π-π stack and its connection to the photophysical properties imparted by the Se oxidation.